RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddA 
           21,609 sequences; 6,263,737 total letters

Searching..................................................done

Query= gi|254780262|ref|YP_003064675.1| 30S ribosomal protein S10
[Candidatus Liberibacter asiaticus str. psy62]
         (104 letters)



>gnl|CDD|144070 pfam00338, Ribosomal_S10, Ribosomal protein S10p/S20e.  This family
           includes small ribosomal subunit S10 from prokaryotes
           and S20 from eukaryotes.
          Length = 97

 Score =  120 bits (303), Expect = 1e-28
 Identities = 50/95 (52%), Positives = 69/95 (72%)

Query: 10  ICLKAFDSRILDSSMREIVLTTKKSGSQIVGPIPFPRSIRRFTVNRSPHVDKKSRDQLEM 69
           I LK++D ++L+S ++ IV   K+ G ++ GPIP P    R TV RSPHVDKKSR+Q EM
Sbjct: 3   IKLKSYDHKLLESYVKFIVEAAKRLGIKVSGPIPLPTKRLRVTVLRSPHVDKKSREQFEM 62

Query: 70  RIYKRLLYIIKPTPQTVDALMKLDIAAGVNVVIKL 104
           R +KRL+ I   TP+TVDAL+++D+  GV+V IKL
Sbjct: 63  RTHKRLIDIYDATPETVDALLRIDLPEGVDVEIKL 97


>gnl|CDD|30400 COG0051, RpsJ, Ribosomal protein S10 [Translation, ribosomal
           structure and biogenesis].
          Length = 104

 Score =  116 bits (291), Expect = 2e-27
 Identities = 57/98 (58%), Positives = 73/98 (74%)

Query: 7   RICICLKAFDSRILDSSMREIVLTTKKSGSQIVGPIPFPRSIRRFTVNRSPHVDKKSRDQ 66
           +I I LK+FD R+LD   REIV T K++G+ + GPIP P    R TV RSPH +K SR+Q
Sbjct: 5   KIRIRLKSFDHRLLDQVCREIVETAKRTGADVKGPIPLPTKRERVTVLRSPHGEKDSREQ 64

Query: 67  LEMRIYKRLLYIIKPTPQTVDALMKLDIAAGVNVVIKL 104
            EMR +KRL+ I+ PTP+TVDALM+LD+ AGV+V IKL
Sbjct: 65  FEMRTHKRLIDIVDPTPKTVDALMRLDLPAGVDVEIKL 102


>gnl|CDD|177057 CHL00135, rps10, ribosomal protein S10; Validated.
          Length = 101

 Score =  101 bits (254), Expect = 4e-23
 Identities = 43/96 (44%), Positives = 67/96 (69%)

Query: 5   NIRICICLKAFDSRILDSSMREIVLTTKKSGSQIVGPIPFPRSIRRFTVNRSPHVDKKSR 64
           N +I I LK+F+  +L+SS ++I+ T  ++ +  VGPIP P   R + V RSPHVDK SR
Sbjct: 6   NAKIRIKLKSFNHELLNSSCKKIIDTASRTNATAVGPIPLPTKRRIYCVLRSPHVDKDSR 65

Query: 65  DQLEMRIYKRLLYIIKPTPQTVDALMKLDIAAGVNV 100
           +  E+R +KR++ I  P+ +T+D+LMKLD+  GV++
Sbjct: 66  EHFEIRTHKRIIDIYYPSSETIDSLMKLDLPPGVDI 101


>gnl|CDD|38531 KOG3321, KOG3321, KOG3321, Mitochondrial ribosomal protein S10
           [Translation, ribosomal structure and biogenesis].
          Length = 175

 Score = 60.8 bits (147), Expect = 9e-11
 Identities = 29/84 (34%), Positives = 43/84 (51%)

Query: 7   RICICLKAFDSRILDSSMREIVLTTKKSGSQIVGPIPFPRSIRRFTVNRSPHVDKKSRDQ 66
            + I L+  D  +LDS    I  T    G  I GP P P+   R+T+ RSP + KKS++ 
Sbjct: 48  LVAIELRGHDKAVLDSYTDFICRTAYYLGIPIKGPEPLPKKRERWTLLRSPFIHKKSKEN 107

Query: 67  LEMRIYKRLLYIIKPTPQTVDALM 90
            E R + RL+ +   T  T+D  +
Sbjct: 108 YERRTHSRLIELYSVTGSTLDTFL 131


>gnl|CDD|36118 KOG0900, KOG0900, KOG0900, 40S ribosomal protein S20 [Translation,
           ribosomal structure and biogenesis].
          Length = 121

 Score = 52.7 bits (126), Expect = 2e-08
 Identities = 26/100 (26%), Positives = 50/100 (50%), Gaps = 2/100 (2%)

Query: 2   TSRNIRICICLKAFDSRILDSSMREIVLTTKKSGSQIVGPIPFPRSIRRFTVNRSPH-VD 60
           T    +I I L +   + L+    ++V   K+   ++ GP+  P  + + T  ++P    
Sbjct: 16  TPEIHKIRITLTSQKVKSLEKVCADLVRGAKEKNLKVKGPVRLPTKVLKITTRKTPCGEG 75

Query: 61  KKSRDQLEMRIYKRLLYIIKPTPQTVDALMKLDIAAGVNV 100
            K+ D+ EMR++KRL+ +  P+ + V  +  + I  GV V
Sbjct: 76  SKTWDRFEMRVHKRLIDLHSPS-EIVKQITSISIEPGVEV 114


>gnl|CDD|144019 pfam00274, Glycolytic, Fructose-bisphosphate aldolase class-I. 
          Length = 348

 Score = 28.8 bits (65), Expect = 0.30
 Identities = 12/38 (31%), Positives = 20/38 (52%)

Query: 23 SMREIVLTTKKSGSQIVGPIPFPRSIRRFTVNRSPHVD 60
          + R+++ TT   G  I G I F  ++ + T +  P VD
Sbjct: 44 AYRQLLFTTPGLGEYISGVILFEETLYQKTDDGKPFVD 81


>gnl|CDD|31343 COG1149, COG1149, MinD superfamily P-loop ATPase containing an
           inserted ferredoxin domain [Energy production and
           conversion].
          Length = 284

 Score = 27.6 bits (61), Expect = 0.88
 Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 1/56 (1%)

Query: 21  DSSMREIVLTTKKSGSQIVGPIPFPRSIRRFTVNRSPHVDKKSRDQLEMR-IYKRL 75
           +    EI    ++ G  I+G IP+ + I    VN  P V+  S++   +    ++L
Sbjct: 225 NLGDSEIEEYCEEEGIPILGEIPYDKDIPEAYVNGEPFVEPDSKEAEAILEEAEKL 280


>gnl|CDD|146362 pfam03686, UPF0146, Uncharacterized protein family (UPF0146).  The
           function of this family of proteins is unknown.
          Length = 127

 Score = 27.0 bits (60), Expect = 1.2
 Identities = 12/38 (31%), Positives = 21/38 (55%), Gaps = 2/38 (5%)

Query: 68  EMRIYK--RLLYIIKPTPQTVDALMKLDIAAGVNVVIK 103
            + IY+   L+Y I+P P+   A++ +  A G  + IK
Sbjct: 64  NISIYEGADLIYSIRPPPELQSAILDVAKAVGAPLYIK 101


>gnl|CDD|31447 COG1255, COG1255, Uncharacterized protein conserved in archaea
           [Function unknown].
          Length = 129

 Score = 26.8 bits (59), Expect = 1.5
 Identities = 12/38 (31%), Positives = 21/38 (55%), Gaps = 2/38 (5%)

Query: 68  EMRIYK--RLLYIIKPTPQTVDALMKLDIAAGVNVVIK 103
            + IY+   L+Y I+P P+   A++ +  A G  + IK
Sbjct: 64  NISIYEGADLIYSIRPPPELQSAILDVAKAVGAPLYIK 101


>gnl|CDD|29941 cd00948, FBP_aldolase_I_a, Fructose-1,6-bisphosphate aldolase.
          The enzyme catalyzes the cleavage of fructose
          1,6-bisphosphate to glyceraldehyde 3-phosphate and
          dihydroxyacetone phosphate (DHAP). This family includes
          proteins found in vertebrates, plants, and bacterial
          plant pathogens. Mutations in the aldolase genes in
          humans cause hemolytic anemia and hereditary fructose
          intolerance. The enzyme is a member of the class I
          aldolase family, which utilizes covalent catalysis
          through a Schiff base formed between a lysine residue
          of the enzyme and ketose substrates..
          Length = 330

 Score = 26.3 bits (58), Expect = 1.8
 Identities = 13/36 (36%), Positives = 19/36 (52%)

Query: 25 REIVLTTKKSGSQIVGPIPFPRSIRRFTVNRSPHVD 60
          RE++ TT   G  I G I F  ++ + T +  P VD
Sbjct: 48 RELLFTTPGLGQYISGVILFEETLYQKTDDGKPFVD 83


>gnl|CDD|132784 cd06874, PX_KIF16B_SNX23, The phosphoinositide binding Phox
          Homology domain of KIF16B kinesin or Sorting Nexin 23. 
          The PX domain is a phosphoinositide (PI) binding module
          present in many proteins with diverse functions such as
          cell signaling, vesicular trafficking, protein sorting,
          and lipid modification, among others. KIF16B, also
          called sorting nexin 23 (SNX23), is a family-3 kinesin
          which harbors an N-terminal kinesin motor domain
          containing ATP and microtubule binding sites, a
          ForkHead Associated (FHA) domain, and a C-terminal PX
          domain. The PX domain of KIF16B  binds to
          phosphatidylinositol-3-phosphate (PI3P) in early
          endosomes and plays a role in the transport of early
          endosomes to the plus end of microtubules. By
          regulating early endosome plus end motility, KIF16B
          modulates the balance between recycling and degradation
          of receptors. SNXs make up the largest group among PX
          domain containing proteins. They are involved in
          regulating membrane traffic and protein sorting in the
          endosomal system. The PX domain of SNXs binds PIs and
          targets the protein to PI-enriched membranes. SNXs
          differ from each other in PI-binding specificity and
          affinity, and the presence of other protein-protein
          interaction domains, which help determine subcellular
          localization and specific function in the endocytic
          pathway.
          Length = 127

 Score = 25.8 bits (57), Expect = 2.3
 Identities = 12/46 (26%), Positives = 19/46 (41%), Gaps = 3/46 (6%)

Query: 39 VGPIPFPRSIRRFTVNRSPHVDKKSRDQLEMRIYKRLLYIIKPTPQ 84
          V  + FP   ++   N+S  V K+ R QLE    +    +    P 
Sbjct: 55 VAALEFPP--KKLFGNKSERVAKERRRQLE-TYLRNFFSVCLKLPA 97


>gnl|CDD|34854 COG5257, GCD11, Translation initiation factor 2, gamma subunit
           (eIF-2gamma; GTPase) [Translation, ribosomal structure
           and biogenesis].
          Length = 415

 Score = 25.2 bits (55), Expect = 3.6
 Identities = 10/22 (45%), Positives = 14/22 (63%)

Query: 81  PTPQTVDALMKLDIAAGVNVVI 102
           P PQT + LM L+I    N++I
Sbjct: 124 PQPQTREHLMALEIIGIKNIII 145


>gnl|CDD|176674 cd07251, Glo_EDI_BRP_like_10, This conserved domain belongs to a
           superfamily including the bleomycin resistance protein,
           glyoxalase I, and type I ring-cleaving dioxygenases.
           This protein family belongs to a conserved domain
           superfamily that is found in a variety of structurally
           related metalloproteins, including the bleomycin
           resistance protein, glyoxalase I, and type I
           ring-cleaving dioxygenases. A bound metal ion is
           required for protein activities for the members of this
           superfamily. A variety of metal ions have been found in
           the catalytic centers of these proteins including
           Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein
           superfamily contains members with or without domain
           swapping.
          Length = 121

 Score = 25.2 bits (56), Expect = 3.6
 Identities = 7/20 (35%), Positives = 12/20 (60%)

Query: 82  TPQTVDALMKLDIAAGVNVV 101
           + + VDA++    AAG  +V
Sbjct: 74  SEEEVDAVLARAAAAGATIV 93


>gnl|CDD|29575 cd02647, nuc_hydro_TvIAG, nuc_hydro_ TvIAG:  Nucleoside
          hydrolases similar to the
          Inosine-adenosine-guanosine-preferring nucleoside
          hydrolase from Trypanosoma vivax.   Nucleoside
          hydrolases cleave the N-glycosidic bond in nucleosides
          generating ribose and the respective base. Nucleoside
          hydrolases vary in their substrate specificity. This
          group contains eukaryotic and bacterial proteins
          similar to the purine specific
          inosine-adenosine-guanosine-preferring nucleoside
          hydrolase (IAG-NH) from T.  vivax.  T. vivax IAG-NH is
          of the order of a thousand to ten thousand fold more
          specific towards the naturally occurring purine
          nucleosides, than towards the pyrimidine nucleosides. .
          Length = 312

 Score = 25.3 bits (55), Expect = 3.7
 Identities = 11/37 (29%), Positives = 15/37 (40%), Gaps = 2/37 (5%)

Query: 19 ILDSSMREIVLTTKKSGSQIVGPIPFPRSIRRFTVNR 55
          ++D   +   +   K GS      PFPRS RR     
Sbjct: 52 LIDRLGQRDAIPVGKGGS--RAVNPFPRSWRRDAAFS 86


>gnl|CDD|146287 pfam03568, Peptidase_C50, Peptidase family C50. 
          Length = 339

 Score = 24.6 bits (54), Expect = 5.4
 Identities = 13/62 (20%), Positives = 23/62 (37%), Gaps = 6/62 (9%)

Query: 36 SQIVGPIPFPRSIRRFTVNRSPHVDK------KSRDQLEMRIYKRLLYIIKPTPQTVDAL 89
            I+        + R + +RSP + +       SRD  E  +      II+   ++V   
Sbjct: 3  EIIISKDTKTLLLSRLSPDRSPIILRLPLDRHNSRDLDESTLLDEFRRIIEEDNESVTTK 62

Query: 90 MK 91
           K
Sbjct: 63 NK 64


>gnl|CDD|176211 cd08249, enoyl_reductase_like, enoyl_reductase_like.  Member
          identified as possible enoyl reductase of the MDR
          family. 2-enoyl thioester reductase (ETR) catalyzes the
          NADPH-dependent dependent conversion of trans-2-enoyl
          acyl carrier protein/coenzyme A (ACP/CoA) to
          acyl-(ACP/CoA) in fatty acid synthesis. 2-enoyl
          thioester reductase activity has been linked in
          Candida tropicalis as essential in maintaining
          mitiochondrial respiratory function. This ETR family is
          a part of the medium chain dehydrogenase/reductase
          family, but lack the zinc coordination sites
          characteristic of the alcohol dehydrogenases in this
          family. NAD(P)(H)-dependent oxidoreductases are the
          major enzymes in the interconversion of alcohols and
          aldehydes, or ketones.  Alcohol dehydrogenase in the
          liver converts ethanol and NAD+ to acetaldehyde and
          NADH, while in yeast and some other microorganisms ADH
          catalyzes the conversion acetaldehyde to ethanol in
          alcoholic fermentation.  ADH is a member of the medium
          chain alcohol dehydrogenase family (MDR), which has a
          NAD(P)(H)-binding domain in a Rossmann fold of a
          beta-alpha form. The NAD(H)-binding region is comprised
          of 2 structurally similar halves, each of which
          contacts a mononucleotide.  The N-terminal catalytic
          domain has a distant homology to GroES.  These proteins
          typically form dimers (typically higher plants,
          mammals) or tetramers (yeast, bacteria), and have 2
          tightly bound zinc atoms per subunit, a catalytic zinc
          at the active site, and a structural zinc in a lobe of
          the catalytic domain.  NAD(H)-binding occurs in the
          cleft between the catalytic  and coenzyme-binding
          domains at the active site, and coenzyme binding
          induces a conformational closing of this cleft.
          Coenzyme binding typically precedes and contributes to
          substrate binding.  Candida tropicalis enoyl thioester
          reductase (Etr1p) catalyzes the NADPH-dependent
          reduction of trans-2-enoyl thioesters in mitochondrial
          fatty acid synthesis. Etr1p forms homodimers with each
          subunit containing a nucleotide-binding Rossmann fold
          domain and a catalytic domain.
          Length = 339

 Score = 24.9 bits (55), Expect = 5.8
 Identities = 7/22 (31%), Positives = 10/22 (45%)

Query: 24 MREIVLTTKKSGSQIVGPIPFP 45
           +  VLT    G  +V  +P P
Sbjct: 1  QKAAVLTGPGGGLLVVVDVPVP 22


>gnl|CDD|144549 pfam00995, Sec1, Sec1 family. 
          Length = 558

 Score = 24.5 bits (54), Expect = 6.1
 Identities = 6/16 (37%), Positives = 11/16 (68%)

Query: 76 LYIIKPTPQTVDALMK 91
          +Y I+PT + VD ++ 
Sbjct: 47 IYFIRPTKENVDRIID 62


>gnl|CDD|132761 cd07076, NR_LBD_GR, Ligand binding domain of the glucocorticoid
          receptor, a member of the nuclear receptor superfamily.
           The ligand binding domain of the glucocorticoid
          receptor (GR): GR is a ligand-activated transcription
          factor belonging to the nuclear receptor superfamily.
          It binds with high affinity to cortisol and other
          glucocorticoids. GR is expressed in almost every cell
          in the body and regulates genes controlling a wide
          variety of processes including the development,
          metabolism, and immune response of the organism. In the
          absence of hormone, the glucocorticoid receptor (GR) is
          complexes with a variety of heat shock proteins in the
          cytosol. The binding of the glucocorticoids results in
          release of the heat shock proteins and transforms it to
          its active state. One mechanism of action of GR is by
          direct activation of gene transcription. The activated
          form of GR forms dimers, translocates into the nucleus,
          and binds to specific hormone responsive elements,
          activating gene transcription. GR can also function as
          a repressor of other gene transcription activators,
          such as NF-kappaB and AF-1 by directly binding to them,
          and bloc king the expression of their activated genes.
          Like other members of the nuclear receptor (NR)
          superfamily of ligand-activated transcription factors,
          GR has a central well conserved DNA binding domain
          (DBD), a variable N-terminal domain, a flexible hinge
          and a C-terminal ligand binding domain (LBD). The LBD
          also functions for dimerization and chaperone protein
          association.
          Length = 247

 Score = 24.1 bits (52), Expect = 7.7
 Identities = 16/58 (27%), Positives = 29/58 (50%), Gaps = 7/58 (12%)

Query: 15 FDSRILDSSMREIVLTTKKSGSQIVGPIPFPRSIRRFTVNRSPHVDKKSRDQLEMRIY 72
          +DS + DS+ R +       G Q+V  + + ++I  F   R+ H+D    DQ+ +  Y
Sbjct: 18 YDSSVPDSTWRIMSTLNMLGGRQVVAAVKWAKAIPGF---RNLHLD----DQMTLLQY 68


>gnl|CDD|133288 cd01888, eIF2_gamma, eIF2-gamma (gamma subunit of initiation factor
           2).  eIF2 is a heterotrimeric translation initiation
           factor that consists of alpha, beta, and gamma subunits.
            The GTP-bound gamma subunit also binds initiator
           methionyl-tRNA and delivers it to the 40S ribosomal
           subunit.  Following hydrolysis of GTP to GDP, eIF2:GDP
           is released from the ribosome.  The gamma subunit has no
           intrinsic GTPase activity, but is stimulated by the
           GTPase activating protein (GAP) eIF5, and GDP/GTP
           exchange is stimulated by the guanine nucleotide
           exchange factor (GEF) eIF2B.  eIF2B is a heteropentamer,
           and the epsilon chain binds eIF2.  Both eIF5 and
           eIF2B-epsilon are known to bind strongly to eIF2-beta,
           but have also been shown to bind directly to eIF2-gamma.
            It is possible that eIF2-beta serves simply as a
           high-affinity docking site for eIF5 and eIF2B-epsilon,
           or that eIF2-beta serves a regulatory role.  eIF2-gamma
           is found only in eukaryotes and archaea.  It is closely
           related to SelB, the selenocysteine-specific elongation
           factor from eubacteria.  The translational factor
           components of the ternary complex, IF2 in eubacteria and
           eIF2 in eukaryotes are not the same protein (despite
           their unfortunately similar names).  Both factors are
           GTPases; however, eubacterial IF-2 is a single
           polypeptide, while eIF2 is heterotrimeric. eIF2-gamma
           is a member of the same family as eubacterial IF2, but
           the two proteins are only distantly related.  This
           family includes translation initiation, elongation, and
           release factors.
          Length = 203

 Score = 24.1 bits (53), Expect = 8.7
 Identities = 8/22 (36%), Positives = 13/22 (59%)

Query: 81  PTPQTVDALMKLDIAAGVNVVI 102
           P PQT + L  L+I    +++I
Sbjct: 121 PQPQTSEHLAALEIMGLKHIII 142


  Database: CddA
    Posted date:  Feb 4, 2011  9:38 PM
  Number of letters in database: 6,263,737
  Number of sequences in database:  21,609
  
Lambda     K      H
   0.326    0.139    0.393 

Gapped
Lambda     K      H
   0.267   0.0673    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,203,312
Number of extensions: 54490
Number of successful extensions: 179
Number of sequences better than 10.0: 1
Number of HSP's gapped: 178
Number of HSP's successfully gapped: 26
Length of query: 104
Length of database: 6,263,737
Length adjustment: 71
Effective length of query: 33
Effective length of database: 4,729,498
Effective search space: 156073434
Effective search space used: 156073434
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (23.5 bits)